High severity · published Mar 18, 2026
CVE-2026-31969
HTSlib CRAM decoder has a heap buffer overflow
8.1
CVSS
0.3%
EPSS
No
On KEV
Description
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
CVSS vector
CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H
Attack vector
Network
Complexity
Low
Privileges
None
User interaction
Required
Confidentiality
None
Integrity
High
Availability
High
Scope
Unchanged
Exploitation
Is it being used?
Exploit prediction (EPSS)0.3% · higher than 28% of CVEs
Exploited in the wildNo evidence yet
CISA KEVNot listed
Ransomware campaign useNot known
Affected products
Which versions
HT
htslib · samtools
< 1.21.1; >= 1.22, < 1.22.2; = 1.23 · source: vendor, NVD
Affected product
HT
htslib
samtools
More from htslib
9.1
CVE-2026-31967
HTSlib CRAM reader has out-of-bounds read due to improper validation of input
9.1
CVE-2026-31966
HTSlib CRAM reader has out-of-bounds read due to improper validation of input
8.8
CVE-2026-31962
HTSlib CRAM reader has heap buffer overflow due to improper validation of input
8.2
CVE-2026-31965
HTSlib CRAM reader has out-of-bounds reads due to improper validation of input
8.1
CVE-2026-31971
HTSlib CRAM decoder vulnerable to buffer overflow